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Add basic_stats and max_pmito_s in Preprocessing #466

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Add basic_stats and max_pmito_s in Preprocessing #466

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6573c1a
fix to the # of cells that are removed
LoveLennone Apr 2, 2023
3416393
Merge branch 'master' into Implement_callers
Ukyeon May 4, 2023
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6 changes: 4 additions & 2 deletions dynamo/preprocessing/Preprocessor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -250,14 +250,16 @@ def standardize_adata(self, adata: AnnData, tkey: str, experiment_type: str) ->
main_info_insert_adata("experiment_type=%s" % adata.uns["pp"]["experiment_type"], "uns['pp']", indent_level=2)

self.convert_layers2csr(adata)
self.collapse_species_adata(adata)
if self.collapse_species_adata:
main_info("applying collapse species adata...")
self.collapse_species_adata(adata)

main_debug("applying convert_gene_name function...")
self.convert_gene_name(adata)

main_debug("making adata observation index unique after gene name conversion...")
self.unique_var_obs_adata(adata)

def _filter_cells_by_outliers(self, adata: AnnData) -> None:
"""Select valid cells based on the method specified as the preprocessor's `filter_cells_by_outliers`.

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6 changes: 2 additions & 4 deletions dynamo/preprocessing/preprocessor_utils.py
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Expand Up @@ -755,11 +755,9 @@ def filter_cells_by_outliers(

if max_pmito_s is not None:
detected_bool = detected_bool & (adata.obs["pMito"] < max_pmito_s)
main_info(
main_debug(
"filtered out %d cells by %f%% of mitochondrial genes for a cell."
% (adata.n_obs - (adata.obs["pMito"] < max_pmito_s).sum(), max_pmito_s),
indent_level=2,
)
% ((adata.obs["pMito"] < max_pmito_s).sum(), max_pmito_s), indent_level=2)

filter_bool = detected_bool if filter_bool is None else np.array(filter_bool) & detected_bool

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